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Dissertation_Final_AditiSengupta.pdf (4.89 MB)

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Studying Methanotrophic Bacterial Diversity in Ohio Soils Using High-Throughput Sequence Analysis

Sengupta, Adti
http://rave.ohiolink.edu/etdc/view?acc_num=osu1436956336

Abstract Details

2015, Doctor of Philosophy, Ohio State University, Environment and Natural Resources.
The net flux of methane (CH4), a biogenic greenhouses gas, into the atmosphere is dependent on feedbacks that exist between the atmosphere and the soil. Aerobic methanotrophic bacteria in soil oxidize CH4 and use it as their sole source of carbon and energy, thereby allowing soils to serve as the only know biological sink of atmospheric methane. However, a clear understanding of the diversity and community composition of these bacteria, as affected by land-use and land-management practices is lacking. The objective of this study was to characterize the diversity of methanotrophs in two contrasting soils in Ohio using the sequencing-by-synthesis technique. In addition to location, the effect of rotation, tillage, and management of soils under grass and forest areas on methanotrophic community was also studied. Several molecular-based high-throughput sequencing techniques were employed. Following a pilot pyrosequencing study, Illumina’s sequencing-by-synthesis approach was used to generate millions of sequences targeting the methanotrophic bacteria. A combination of four primer sets targeting the whole community 16S rRNA, the 16S rRNA gene region of Type I and Type II methanotrophs, and the functional pmoA gene (a subunit of the particulate methane monooxygenase gene) were used. Software packages including Mothur, QIIME (Quantitative Insights Into Microbial Ecology), and R were used to study community diversity and abundance in soils under no-till continuous corn, no-till corn-soybean, plow-till continuous-corn, plow-till corn-soybean, grass, and forest. A variety of methanotrophic bacterial operational taxonomic units (OTUs) were identified across different land-uses and management, representing diverse genera of methanotrophs. On average, 2% of sequences represented methantrophs OTUs in the 16S rRNA datasets, while the pmoA dataset was compared to a reference database which classified all the sequences as methanotrophic OTUs. Community diversity estimators showed that a combination of community richness and evenness contributed to the methanotrophic diversity. In addition to commonly reported methanotrophic genera, this study also noted the presence of Verrucomicrobial methanotrophic OTUs, non-methanotrophic methylotroph OTUs, and OTUs representing Upland Soil Clusters. For most datasets, no-till soils had higher diversity than plow-till soils. The community composition of both agricultural practices were distinctly different from forest and grass areas. Due to the fact that forest soils were undisturbed, the highest number of different species was generally recovered from these soils. Among the variables analyzed, location was dominant, followed by tillage and rotation. The pmoA dataset showed that even over a long period of time (>50 years), soil methanotrophy function was governed by soil type. It can be concluded that despite soil disturbance, the inherent functioning of microbes in these soils is possibly more impacted by soil type, that is a reflection of its geographical location, followed by land-use. This dissertation adds to knowledge of land-use and land-management practices that can be employed on a long-term basis to increase biological fixation of CH4 gas. On a broader level, this study of methanotrophic diversity in soils has the potential to help develop climate change mitigation strategies with respect to globally shifting soils to become increasingly active as CH4 sinks.
Warren Dick, Dr. (Advisor)
300 p.
Agriculture; Microbiology; Soil Sciences
Methanotrophs; high-throughput sequencing; no-till; plow-till; long-term agricultural experiment; methane oxidation; land use; soil type

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Citations

  • Sengupta, A. (2015). Studying Methanotrophic Bacterial Diversity in Ohio Soils Using High-Throughput Sequence Analysis [Doctoral dissertation, Ohio State University]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=osu1436956336

    APA Style (7th edition)

  • Sengupta, Adti. Studying Methanotrophic Bacterial Diversity in Ohio Soils Using High-Throughput Sequence Analysis . 2015. Ohio State University, Doctoral dissertation. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=osu1436956336.

    MLA Style (8th edition)

  • Sengupta, Adti. "Studying Methanotrophic Bacterial Diversity in Ohio Soils Using High-Throughput Sequence Analysis ." Doctoral dissertation, Ohio State University, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=osu1436956336

    Chicago Manual of Style (17th edition)

osu1436956336
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This open access ETD is published by The Ohio State University and OhioLINK.